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insertion/deletion:how to weigh in a DNA sequence matrix?

Zhang Daming zhangdm at ns.ibcas.ac.cn
Mon Nov 10 02:44:26 EST 1997

Dear colleagues,
I have a data matrix of ITS sequences in a tribe of Liliaceae, in which
several insertion/deletions, 4-16 bp long, appear informative (existed
in several taxa, seemingly as synapomorphis ). Unfortunately, when I
applied PAUP to them , aligned each single base involved as either "-"
or "?",  I found that  the ins/dels were apparently un-informative and
somewhat homoplasy. Comparing to base substitution, "structural
variations", like ins/del, inversion or translocation, would be much
rarer, and should be somehow weighed over other characters. I tried
weighing them in different quantity, and even treating them as extra
characters at the matrix before using PAUP program. But the results
looked not improved. Could anyone tell me how to deal with such problem?
Any help and information would be appreciated.
Daming Zhang, Ph.D.
Laboratory of Systematic & Evolutionary Botany,
Institute of Botany,
Chinese Academy of Sciences
20 Nanxincun, Xiangshan
Beijing 100093,  China
Ph. +(86-10)62591431 ext.6097 (O)
    +(86-10)62591431 ext.6445 (L)
    +(86-10)62591431 ext.6397 (H)
E-mail:  zhangdm at ns.ibcas.ac.cn
Fax: +(86-10)62590843
Personal interests: phylogenesis, evolution, DNA sequencing,
      in situ hybridization, genomic library, chromosome

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